Ppp1r9b (protein phosphatase 1, regulatory subunit 9B) - Rat Genome Database

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Gene: Ppp1r9b (protein phosphatase 1, regulatory subunit 9B) Rattus norvegicus
Analyze
Symbol: Ppp1r9b
Name: protein phosphatase 1, regulatory subunit 9B
RGD ID: 632281
Description: Exhibits several functions, including D2 dopamine receptor binding activity; enzyme binding activity; and ion channel binding activity. Involved in several processes, including cellular response to epidermal growth factor stimulus; pallium development; and positive regulation of protein localization to cell periphery. Localizes to several cellular components, including dendritic spine; growth cone; and postsynaptic density. Biomarker of Parkinson's disease. Orthologous to human PPP1R9B (protein phosphatase 1 regulatory subunit 9B); INTERACTS WITH (S)-amphetamine; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Neb2; neurabin 2; neurabin-2; neurabin-II; neural tissue-specific F-actin-binding protein II; nuerabin 2; p130; PP1bp134; spinophilin
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21079,938,055 - 79,954,085 (+)NCBI
Rnor_6.0 Ensembl1082,800,704 - 82,816,731 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01082,800,704 - 82,816,735 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01082,616,223 - 82,632,356 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41083,674,797 - 83,690,639 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11083,689,166 - 83,705,009 (+)NCBI
Celera1078,712,214 - 78,727,757 (+)NCBICelera
Cytogenetic Map10q26NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
actin filament depolymerization  (IEP)
actin filament organization  (IBA,ISO)
aging  (IEP)
calcium-mediated signaling  (IBA,ISO)
cell migration  (ISO,ISS)
cellular response to drug  (IEP)
cellular response to epidermal growth factor stimulus  (IEP)
cellular response to estradiol stimulus  (IEP)
cellular response to morphine  (ISO,ISS)
cellular response to organic cyclic compound  (IEP)
cellular response to peptide  (IEP)
cerebral cortex development  (IEP)
dendrite development  (ISO)
developmental process involved in reproduction  (IEP)
filopodium assembly  (ISO,ISS)
hippocampus development  (IEP)
learning  (IEP)
male mating behavior  (IEP)
modulation of chemical synaptic transmission  (IEA)
negative regulation of cell growth  (ISO)
negative regulation of phosphoprotein phosphatase activity  (IDA,IMP)
neuron projection development  (IBA)
positive regulation of cellular protein localization  (IDA)
positive regulation of protein localization to actin cortical patch  (IMP)
positive regulation of protein localization to plasma membrane  (IDA)
protein localization to actin cytoskeleton  (IMP)
protein localization to cell periphery  (IMP)
protein phosphorylation  (IEA)
regulation of cell population proliferation  (IEA)
regulation of opioid receptor signaling pathway  (ISO,ISS)
regulation of protein phosphorylation  (ISO)
reproductive system development  (IEP)
response to amino acid  (IEP)
response to amphetamine  (IEP)
response to clozapine  (IEP)
response to drug  (IEP)
response to estradiol  (IEP)
response to immobilization stress  (IEP)
response to kainic acid  (IEP)
response to L-phenylalanine derivative  (IEP)
response to nicotine  (IEP)
response to organic cyclic compound  (IEP)
response to organonitrogen compound  (IEP)
response to prostaglandin E  (IEP)
response to steroid hormone  (IEP)

Cellular Component

References

References - curated
1. Aigelsreiter A, etal., Br J Cancer. 2013 May 14;108(9):1830-7. doi: 10.1038/bjc.2013.165. Epub 2013 Apr 16.
2. Allen PB, etal., Proc Natl Acad Sci U S A 1997 Sep 2;94(18):9956-61.
3. Alves SE, etal., Synapse. 2002 Aug;45(2):143-51.
4. Aydin C, etal., Neuropharmacology. 2012 Dec;63(8):1335-45. doi: 10.1016/j.neuropharm.2012.08.016. Epub 2012 Aug 31.
5. Barnes AP, etal., Brain Res Mol Brain Res. 2004 May 19;124(2):105-13.
6. Boikess SR, etal., Neurosci Lett. 2010 Jan 18;469(1):49-54. doi: 10.1016/j.neulet.2009.11.042. Epub 2009 Nov 20.
7. Brown AM, etal., Eur J Neurosci. 2005 Jul;22(1):247-56.
8. Brown AM, etal., J Biol Chem. 2008 May 23;283(21):14286-94. doi: 10.1074/jbc.M801377200. Epub 2008 Mar 26.
9. Buchsbaum RJ, etal., J Biol Chem 2003 May 23;278(21):18833-41. Epub 2003 Jan 16.
10. Burks SR, etal., Neuroscience. 2007 May 25;146(3):1117-27. Epub 2007 Apr 6.
11. Burnett PE, etal., Proc Natl Acad Sci U S A. 1998 Jul 7;95(14):8351-6.
12. Carmody LC, etal., FASEB J. 2008 Jun;22(6):1660-71. doi: 10.1096/fj.07-092841. Epub 2008 Jan 23.
13. Critchlow HM, etal., Mol Cell Neurosci. 2006 Aug;32(4):356-65. Epub 2006 Jul 17.
14. Dean SL, etal., Endocrinology. 2012 Nov;153(11):5415-27. doi: 10.1210/en.2012-1350. Epub 2012 Oct 9.
15. Estevez-Garcia P, etal., Clin Cancer Res. 2013 Jul 15;19(14):3925-35. doi: 10.1158/1078-0432.CCR-13-0057. Epub 2013 May 31.
16. Ferrer I, etal., Cell Cycle. 2011 Jun 15;10(12):1948-55. Epub 2011 Jun 15.
17. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
18. GOA data from the GO Consortium
19. Goel M, etal., Pflugers Arch. 2005 Oct;451(1):87-98. Epub 2005 Jul 16.
20. Holder MK and Mong JA, Horm Behav. 2010 Aug;58(3):519-25. doi: 10.1016/j.yhbeh.2010.04.006. Epub 2010 Apr 24.
21. Hsieh-Wilson LC, etal., J Biol Chem 2003 Jan 10;278(2):1186-94. Epub 2002 Nov 1.
22. Ide N, etal., Biochem Biophys Res Commun. 1998 Mar 6;244(1):258-62.
23. Ladurelle N, etal., Psychopharmacology (Berl). 2012 Jun;221(3):493-509. doi: 10.1007/s00213-011-2597-5. Epub 2011 Dec 8.
24. Law AJ, etal., Am J Psychiatry. 2004 Oct;161(10):1848-55.
25. Ma P, etal., PLoS One. 2015 Mar 18;10(3):e0119496. doi: 10.1371/journal.pone.0119496. eCollection 2015.
26. MacMillan LB, etal., J Biol Chem. 1999 Dec 10;274(50):35845-54.
27. MGD data from the GO Consortium
28. Molina-Pinelo S, etal., J Pathol. 2011 Sep;225(1):73-82. doi: 10.1002/path.2905. Epub 2011 May 19.
29. Nakanishi H, etal., J Cell Biol 1997 Nov 17;139(4):951-61.
30. Orlowski D, etal., Stress. 2012 Sep;15(5):514-23. doi: 10.3109/10253890.2011.643516. Epub 2012 Jan 10.
31. Ottis P, etal., PLoS One. 2013 Sep 19;8(9):e75112. doi: 10.1371/journal.pone.0075112. eCollection 2013.
32. Palavicini JP, etal., Cell Death Dis. 2013 Jun 13;4:e667. doi: 10.1038/cddis.2013.183.
33. Penzes P, etal., Neuron. 2001 Jan;29(1):229-42.
34. Ragusa MJ, etal., FEBS Lett. 2011 Jan 3;585(1):36-40. doi: 10.1016/j.febslet.2010.11.022. Epub 2010 Nov 19.
35. Ragusa MJ, etal., Nat Struct Mol Biol. 2010 Apr;17(4):459-64. doi: 10.1038/nsmb.1786. Epub 2010 Mar 21.
36. RGD automated data pipeline
37. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
38. RGD automated import pipeline for gene-chemical interactions
39. Satoh A, etal., J Biol Chem 1998 Feb 6;273(6):3470-5.
40. Schang AL, etal., Endocrinology. 2011 Feb;152(2):568-80. doi: 10.1210/en.2010-0840. Epub 2010 Dec 1.
41. Smith FD, etal., J Biol Chem 1999 Jul 9;274(28):19894-900.
42. Stankovic KM, etal., Laryngoscope. 2008 May;118(5):881-9. doi: 10.1097/MLG.0b013e31816b4b6f.
43. Stephens DJ and Banting G, Biochem J. 2000 Jan 15;345 Pt 2:185-94.
44. Stephens DJ and Banting G, J Biol Chem. 1999 Oct 15;274(42):30080-6.
45. Terry-Lorenzo RT, etal., J Biol Chem 2002 Aug 2;277(31):27716-24.
46. Terry-Lorenzo RT, etal., J Biol Chem 2002 Nov 29;277(48):46535-43. Epub 2002 Sep 21.
47. Todd BJ, etal., Dev Neurobiol. 2007 Feb 15;67(3):304-15.
48. Wright CL, etal., Dev Neurobiol. 2008 Oct;68(12):1406-19. doi: 10.1002/dneu.20665.
49. Yildirim M, etal., Exp Neurol. 2008 Apr;210(2):339-48. Epub 2007 Nov 21.
50. Zhao L, etal., J Pharmacol Exp Ther. 2006 Dec;319(3):1124-32. Epub 2006 Sep 1.
Additional References at PubMed
PMID:10194355   PMID:10922077   PMID:11154706   PMID:11278317   PMID:12477932   PMID:15218143   PMID:15228588   PMID:15514983   PMID:15743906   PMID:15793568   PMID:15996550   PMID:16930415  
PMID:17464283   PMID:18439408   PMID:19151759   PMID:19609226   PMID:20124353   PMID:20385205   PMID:24625528   PMID:25750125   PMID:27890541   PMID:29383693  


Genomics

Comparative Map Data
Ppp1r9b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21079,938,055 - 79,954,085 (+)NCBI
Rnor_6.0 Ensembl1082,800,704 - 82,816,731 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01082,800,704 - 82,816,735 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01082,616,223 - 82,632,356 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41083,674,797 - 83,690,639 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11083,689,166 - 83,705,009 (+)NCBI
Celera1078,712,214 - 78,727,757 (+)NCBICelera
Cytogenetic Map10q26NCBI
PPP1R9B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1750,133,737 - 50,150,677 (-)EnsemblGRCh38hg38GRCh38
GRCh381750,133,737 - 50,150,677 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371748,211,101 - 48,228,038 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361745,566,100 - 45,582,876 (-)NCBINCBI36hg18NCBI36
Build 341745,567,694 - 45,582,873NCBI
Celera1744,671,218 - 44,687,998 (-)NCBI
Cytogenetic Map17q21.33NCBI
HuRef1743,578,978 - 43,595,756 (-)NCBIHuRef
CHM1_11748,275,417 - 48,292,199 (-)NCBICHM1_1
Ppp1r9b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391194,882,038 - 94,897,724 (+)NCBIGRCm39mm39
GRCm39 Ensembl1194,881,861 - 94,897,725 (+)Ensembl
GRCm381194,991,212 - 95,006,898 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1194,991,035 - 95,006,899 (+)EnsemblGRCm38mm10GRCm38
MGSCv371194,852,526 - 94,868,212 (+)NCBIGRCm37mm9NCBIm37
MGSCv361194,807,302 - 94,822,974 (+)NCBImm8
Celera11104,604,585 - 104,620,251 (+)NCBICelera
Cytogenetic Map11DNCBI
Ppp1r9b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545111,516,548 - 11,530,830 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545111,516,548 - 11,530,263 (+)NCBIChiLan1.0ChiLan1.0
PPP1R9B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11749,098,089 - 49,129,659 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1749,098,089 - 49,126,932 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01744,224,007 - 44,240,906 (-)NCBIMhudiblu_PPA_v0panPan3
PPP1R9B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1926,135,982 - 26,152,303 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl926,137,464 - 26,151,810 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha925,529,124 - 25,544,951 (-)NCBI
ROS_Cfam_1.0926,930,469 - 26,946,307 (-)NCBI
UMICH_Zoey_3.1925,698,261 - 25,714,094 (-)NCBI
UNSW_CanFamBas_1.0925,956,940 - 25,972,777 (-)NCBI
UU_Cfam_GSD_1.0926,086,858 - 26,102,695 (-)NCBI
Ppp1r9b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560225,560,948 - 25,577,086 (-)NCBI
SpeTri2.0NW_00493649011,497,389 - 11,514,191 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PPP1R9B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1226,319,124 - 26,336,562 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11226,319,123 - 26,337,089 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21226,358,245 - 26,375,863 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PPP1R9B
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11643,188,400 - 43,205,621 (+)NCBI
ChlSab1.1 Ensembl1643,188,022 - 43,205,680 (+)Ensembl
Vero_WHO_p1.0NW_02366607713,904,402 - 13,921,606 (+)NCBI
Ppp1r9b
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247956,124,273 - 6,137,776 (-)NCBI

Position Markers
BF405560  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21079,935,928 - 79,936,106 (+)MAPPER
Rnor_6.01082,798,567 - 82,798,744NCBIRnor6.0
Rnor_5.01082,614,086 - 82,614,263UniSTSRnor5.0
RGSC_v3.41083,672,660 - 83,672,837UniSTSRGSC3.4
Celera1078,709,633 - 78,709,810UniSTS
RH 3.4 Map10720.3UniSTS
Cytogenetic Map10q31UniSTS
BE117171  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21079,944,130 - 79,944,307 (+)MAPPER
Rnor_6.01082,806,781 - 82,806,957NCBIRnor6.0
Rnor_5.01082,622,402 - 82,622,578UniSTSRnor5.0
RGSC_v3.41083,680,945 - 83,681,121UniSTSRGSC3.4
Celera1078,717,804 - 78,717,980UniSTS
RH 3.4 Map10719.0UniSTS
Cytogenetic Map10q31UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10642907599492409Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109841807108540162Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101482789492423564Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014827894107857673Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014827894110992275Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)1020170031102897474Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102152390683549467Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)12152390690312401Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102152390690312401Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102290149793886300Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1023861015112626471Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)1027237530101482600Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1027237530102427718Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)103618592995845311Rat
2317042Aia20Adjuvant induced arthritis QTL 203.38joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)104051404485514044Rat
2317043Aia7Adjuvant induced arthritis QTL 73.82joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)104051404485514044Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1041260363106105607Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1041260363107857673Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1041260363107857673Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1043289657108540162Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104370495588704955Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104659302198939209Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104684834691848346Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104684834691848346Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104684834691848346Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)105063833795638337Rat
2293652Bmd22Bone mineral density QTL 224.90.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)105128920384596393Rat
2293669Bmd33Bone mineral density QTL 334.50.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)105128920384596393Rat
2293679Bmd30Bone mineral density QTL 303.50.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)105128920384596393Rat
2293705Bmd25Bone mineral density QTL 257.10.0001femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)105128920384596393Rat
7207811Bmd90Bone mineral density QTL 905.2femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)105128920384596393Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105310471898104718Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1053621375112626471Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1053621375112626471Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105362581598939209Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105363748594807701Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)1055224855100224855Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1055678976112626471Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)1055679084102427604Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1056698730101698730Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1060450007105450007Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1060875260105875260Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1060875260105875260Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1060875260105875260Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1062096293107096293Rat
70363Bp71Blood pressure QTL 710.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)106464817584601269Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)1064648175101691360Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)1064648175102149713Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1064648175102149713Rat
61402Niddm3Non-insulin dependent diabetes mellitus QTL 34.58blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)106464831185513822Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1065590122110590122Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1065992275110992275Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1065992275110992275Rat
7387312Bw125Body weight QTL 12530.0047retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight (CMO:0000356)1067880046112626471Rat
1581559Eae18Experimental allergic encephalomyelitis QTL 180.00002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1067988218110992091Rat
2298481Eau9Experimental allergic uveoretinitis QTL 90.0169uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)106830503785514044Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1069123603101482600Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1069385595112626471Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1069385595112626471Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1070166960112626471Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1070800069112626471Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1071692298112626471Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1073008136112626471Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1073008136112626471Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1073008136112626471Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1073467158112626471Rat
2306793Ean5Experimental allergic neuritis QTL 54.7nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)107504539197308358Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1075544754112626471Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1075544754112626471Rat
12880053Cm104Cardiac mass QTL 1040.009heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)107598366286419171Rat
1358188Ept9Estrogen-induced pituitary tumorigenesis QTL 93.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107598380599492217Rat
2292617Ept18Estrogen-induced pituitary tumorigenesis QTL 183.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107598380599492217Rat
12880050Am10Aortic mass QTL 100.016aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)107705574186962563Rat
1579919Bp281Blood pressure QTL 2810.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107705574198282519Rat
631537Oia4Oil induced arthritis QTL 4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)107834302790042115Rat
2325836Bp346Blood pressure QTL 3460.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107897027986962563Rat
10450495Bp383Blood pressure QTL 3830.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107897027998282519Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1078970279112626471Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1079927661112626471Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1080239190112626471Rat
724516Uae17Urinary albumin excretion QTL 173.6urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)108094611088200662Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)1081515116101758478Rat
1358915Stresp7Stress response QTL 73.52blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)108164977590297007Rat
634354Rends3Renal damage susceptibility QTL 30.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)108267523388141097Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:215
Count of miRNA genes:144
Interacting mature miRNAs:158
Transcripts:ENSRNOT00000005498
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 42 38 22 19 22 2 4 74 33 41 11 2
Low 1 19 19 19 6 7 2 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000089497   ⟹   ENSRNOP00000074026
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1082,800,704 - 82,816,731 (+)Ensembl
RefSeq Acc Id: NM_053474   ⟹   NP_445926
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,938,066 - 79,954,085 (+)NCBI
Rnor_6.01082,800,704 - 82,816,735 (+)NCBI
Rnor_5.01082,616,223 - 82,632,356 (+)NCBI
RGSC_v3.41083,674,797 - 83,690,639 (+)RGD
Celera1078,712,214 - 78,727,757 (+)RGD
Sequence:
RefSeq Acc Id: XM_039086990   ⟹   XP_038942918
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21079,938,055 - 79,952,554 (+)NCBI
Protein Sequences
Protein RefSeqs NP_445926 (Get FASTA)   NCBI Sequence Viewer  
  XP_038942918 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB72005 (Get FASTA)   NCBI Sequence Viewer  
  AAC05183 (Get FASTA)   NCBI Sequence Viewer  
  AAI60878 (Get FASTA)   NCBI Sequence Viewer  
  O35274 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_445926   ⟸   NM_053474
- UniProtKB: O35274 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074026   ⟸   ENSRNOT00000089497
RefSeq Acc Id: XP_038942918   ⟸   XM_039086990
- Peptide Label: isoform X1
Protein Domains
PDZ

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13697614
Promoter ID:EPDNEW_R8139
Type:initiation region
Name:Ppp1r9b_1
Description:protein phosphatase 1, regulatory subunit 9B
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01082,800,655 - 82,800,715EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:632281 AgrOrtholog
BIND 130595
  130600
Ensembl Genes ENSRNOG00000052113 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000074026 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000089497 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.30.42.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7376917 IMAGE-MGC_LOAD
InterPro NEB2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neurabin-1/2_PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Neurabin-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:84686 UniProtKB/Swiss-Prot
MGC_CLONE MGC:188268 IMAGE-MGC_LOAD
NCBI Gene 84686 ENTREZGENE
PANTHER PTHR16154 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR16154:SF24 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ_5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ppp1r9b PhenoGen
PROSITE PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50156 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt B1H262_RAT UniProtKB/TrEMBL
  NEB2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Ppp1r9b  protein phosphatase 1, regulatory subunit 9B  Neb2  nuerabin 2  Symbol and Name updated 1299863 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localized in the PSD (post-synaptic density) 625568
gene_cellular_localization localized in the PSD (post-synaptic density) 625590
gene_cellular_localization localized in the PSD (post-synaptic density) 625591
gene_cellular_localization localized in the PSD (post-synaptic density) 625592
gene_domains contains a PSD95/DLG/zo-1(PDZ) domain 625568
gene_domains contains a PSD95/DLG/zo-1(PDZ) domain 625590
gene_domains contains a PSD95/DLG/zo-1(PDZ) domain 625591
gene_domains contains a PSD95/DLG/zo-1(PDZ) domain 625592
gene_expression purified from rat brain neural tissues 625592
gene_function binds to protein phosphatase1 625568
gene_function binds to protein phosphatase1 625590
gene_function binds to protein phosphatase1 625591
gene_function binds to protein phosphatase1 625592
gene_function binds to actin filaments 625568
gene_function binds to actin filaments 625590
gene_function binds to actin filaments 625591
gene_function binds to actin filaments 625592
gene_physical_interaction interacts with protein phosphatase type 1 alpha and type 1 gamma isoform 1 to regulate synaptic transmission 625568
gene_physical_interaction interacts with protein phosphatase type 1 alpha and type 1 gamma isoform 1 to regulate synaptic transmission 625590
gene_physical_interaction interacts with protein phosphatase type 1 alpha and type 1 gamma isoform 1 to regulate synaptic transmission 625591
gene_physical_interaction interacts with protein phosphatase type 1 alpha and type 1 gamma isoform 1 to regulate synaptic transmission 625592
gene_physical_interaction binds to protein phosphatase1  
gene_process regulates synaptic activity by binding to protein phosphatase type 1 alpha and gamma isoform 1 present in the PSD 625568
gene_process regulates synaptic activity by binding to protein phosphatase type 1 alpha and gamma isoform 1 present in the PSD 625591
gene_process involved in vesicular trafficking in developing and developed neurons and formation and maintenance of synaptic junctions 625568
gene_process involved in vesicular trafficking in developing and developed neurons and formation and maintenance of synaptic junctions 625590
gene_process involved in vesicular trafficking in developing and developed neurons and formation and maintenance of synaptic junctions 625591
gene_process involved in vesicular trafficking in developing and developed neurons and formation and maintenance of synaptic junctions 625592
gene_process interacts with protein phosphatase type 1 alpha and type 1 gamma isoform 1 to regulate synaptic transmission  
gene_product 4.6 kb in size 625568
gene_product 4.6 kb in size 625590
gene_product 4.6 kb in size 625591
gene_product 4.6 kb in size 625592
gene_regulation phosphorylated by PKA 625568
gene_regulation phosphorylated by PKA 625591
gene_regulation regulates synaptic activity by binding to protein phosphatase type 1 alpha and gamma isoform 1 present in the PSD and can be phosphorylated by PKA 625568
gene_regulation regulates synaptic activity by binding to protein phosphatase type 1 alpha and gamma isoform 1 present in the PSD and can be phosphorylated by PKA 625590
gene_regulation regulates synaptic activity by binding to protein phosphatase type 1 alpha and gamma isoform 1 present in the PSD and can be phosphorylated by PKA 625591
gene_regulation regulates synaptic activity by binding to protein phosphatase type 1 alpha and gamma isoform 1 present in the PSD and can be phosphorylated by PKA 625592